Demo datasets for: ArtiaX: An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX

ArtiaX is an open-source extension of the molecular visualisation program ChimeraX and is primarily intended for visualization and processing of cryo-electron tomography data. It allows easy import and export of particle lists in various formats and performant interaction with the data on screen and in virtual reality.

This dataset contains cryo-electron tomograms, particle lists, demo command scripts and scripts for performance measurements used for the creation of figures and measurements in the paper "ArtiaX: An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX"

Contents

• empiar_10304.zip -- used for Figure 2 and Supplementary Video 1 of the companion paper
  • Tomogram 10 of the EMPIAR-10304 dataset¹ reconstructed using super-sampling SART
  • A particle list containing particle positions and poses determined using template matching
  • A lowpass-filtered map of EMD-10211¹ used for surface display
     
• mycoplasma_genitalium.zip -- used for Figures 1, 4, 5 and 6, as well as Supplementary Videos 2, 3 and 4 of the companion paper
  • A tomogram of a Mycoplasma genitalium cell² reconstructed using super-sampling SART
  • A demo dataset comprising particle lists, segmentation maps and a demo script related to the above tomogram
  • Python scripts for measuring ChimeraX rendering performance of the demo dataset scene.

References

1. Eisenstein F, Danev R, Pilhofer M (2019) Improved applicability and robustness of fast cryo-electron tomography data acquisition. Journal of Structural Biology 208:107–114.

2. Seybert A, Gonzalez-Gonzalez L, Scheffer MP, Lluch-Senar M, Mariscal AM, Querol E, Matthaeus F, Piñol J, Frangakis AS (2018) Cryo-electron tomography analyses of terminal organelle mutants suggest the motility mechanism of Mycoplasma genitalium. Molecular Microbiology 108:319–329.